GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aacS in Novosphingobium barchaimii LL02

Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_059150936.1 V474_RS07610 acyl--CoA ligase

Query= reanno::acidovorax_3H11:Ac3H11_3009
         (578 letters)



>NCBI__GCF_001046635.1:WP_059150936.1
          Length = 545

 Score =  234 bits (597), Expect = 7e-66
 Identities = 171/549 (31%), Positives = 262/549 (47%), Gaps = 23/549 (4%)

Query: 30  TIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLGMGLTPGDRVGIWSH 89
           T+G        R  +R+A+V     RR  YA L  +A   A AL  MG+ PGD VG+   
Sbjct: 9   TMGEMIRSSGQRFADRDAIV--FPDRRLGYADLNRKARDWARALAAMGVKPGDNVGLLLP 66

Query: 90  NNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTS-DYLGMLR 148
              +++         G V V +N  Y+ +E+ + +       +++  +     D+   L 
Sbjct: 67  TCLDFITAFYGITMTGAVAVPVNARYQASELGFVVADADLVAIITTGKVADGLDFSARLE 126

Query: 149 ELAPEW-QGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTELIARG-----NAA 202
              P   Q   P  L   + P+L+++V +D+        P L+     +A+G     +  
Sbjct: 127 AAMPSLTQSGDPWALSLPEAPRLRSIVCLDERCA-----PYLVPANAALAKGAKIAEDEI 181

Query: 203 DPRLAQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMKLTPADRLCI 262
           D R+  VA      D   I +TSGTT  PKGA ++HR  + N   +G   + T  D++  
Sbjct: 182 DARIDAVAP----QDTAMILYTSGTTANPKGAMISHRAQVANSRGLGVRYECTEEDKVWS 237

Query: 263 PVPLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAEL- 321
           P+P++H  G++   +     G  +  P   FD    L+ +  E  T  +      + +L 
Sbjct: 238 PLPIFHIAGILPMTMILDIGGVYMTIPR--FDAGVGLEMLGREGATIAYPSFVTIMQDLI 295

Query: 322 DHPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDT 381
            HP F + +LS LR      +  P  +   V E M        YG+TE +     S    
Sbjct: 296 THPTFKDTDLSRLRIMNSNFAVQPEWIKLAVAEAMPHTIQVGTYGLTEGAGTVSTSRLSD 355

Query: 382 PLSKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAID 441
               R    G      +V+IVDP+TGA    G+ GE    G +V+ GY+    KT EAI 
Sbjct: 356 SYEVRTGRCGVPLEEWQVRIVDPETGADCGPGEHGEIVLGGPNVLKGYYNAPEKTAEAIR 415

Query: 442 EGGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVP 501
           +G W  +GD+ ++DA G V   GR KDM+  GGEN+   EIE  L  HP V+  QVVG+P
Sbjct: 416 DG-WFFSGDIGSIDANGNVMFHGRTKDMLKVGGENVAAAEIEAMLQTHPAVKLAQVVGLP 474

Query: 502 DQKYGEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFK 561
           D +Y E   A++    G   +E ++   CKG+IA +KVPR+IRFV  +PM+ T KIQKF+
Sbjct: 475 DDRYAEVPAAFVELAEGAAASEQELIDHCKGRIAGFKVPRHIRFVEEWPMS-TSKIQKFR 533

Query: 562 IRDEMKDQL 570
           +R+ +  +L
Sbjct: 534 LREGLIAEL 542


Lambda     K      H
   0.320    0.136    0.412 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 727
Number of extensions: 33
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 578
Length of database: 545
Length adjustment: 36
Effective length of query: 542
Effective length of database: 509
Effective search space:   275878
Effective search space used:   275878
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory